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A Prediction Tested

Several themes have been doing the rounds lately. The origin of organelles, standards of evidence, common descent, the role of phylogenetic analysis, and the meaning of ‘prediction’ in science. Here’s a case study/rambling discourse that links a few themes.

Researching an answer to a separate question (I do try), I was struck by a thought about RecA. RecA (also going by the names RAD51, Dmc1 and RADA in different groups, for historical reasons) is a ubiquitous group of proteins involved in homologous DNA repair. That’s a process whereby a break in DNA can be ‘patched’ if a homologous sequence can be located. Matching sequence either side of the gap is aligned (by nothing more sophisticated than the binding energy of DNA complementarity) and then a DNA polymerase template-copies from the intact strand to the broken one between the two complementary sequences. Both accidental and deliberate breaks are repaired by this, hence it is involved both in maintaining DNA integrity and in the more ‘orchestrated’ process of crossover formation in meiosis.

Because this process relies on quite a high degree of complementarity, it works best on sister chromosomes – those recently replicated, within the current cell cycle, and hence clearly commonly descended. This is all a prokaryote has to work with, outside of instances of LGT. In eukaryotic diploids, the donor for repair can be the homologous diploid chromosome (that’s a terminological confusion: the chromosome pair with the greatest amount of homology is actually not the homologous pair, but the sister pair). But even in diploids, the sister is ‘preferred’ for repair – when not available, the normal repair pathway is ‘nonhomologous end joining’, which simply splices the break. An exception to this is during crossover of meiosis. Most crossovers form between homologues, not sisters.

So, thinks I, if chloroplasts and mitochondria evolved from bacteria, their RecA equivalents should be more like those of bacteria than archaea. To the internet!

It so happens that all these proteins are, in the modern eukaryote, held in nuclear DNA. So in a plant, you’ve got your RAD51s, plus Dmc1 specific to meiosis, but you’ve also got RecA proteins targeting, respectively, mitochondria and chloroplasts. RECA1 heads for chloroplasts, RECA3 for mitochondria. There’s also RECA2 which goes to both.

More specific and comprehensive phylogenetic analysis reveals quite a complex picture. Nonetheless, the Lin paper notes a ‘striking’ sequence similarity between the recA genes of plants and protists and those of the bacteria from which they are presumed to have come. There is a healthy 61% sequence match between RECA1 and the RecA of cyanobacteria. Sequence identity for RECA3/bacteria is not so high, but interestingly, ArabidopsisRECA3 can complement E. coli deficient in bacterial recA. E. coli are Gammaproteobacteria, not Alphaproteobacteria as is thought to be the group from which mitochondria came, but still not a million miles away. That’s not conclusive of a common origin, but is a noteworthy fact, consistent with structural conservation.

And that, really, is where I was headed. I started from the hypothesis that mitochondria and chloroplasts originated as bacteria. A prediction of that hypothesis is that organelle-targeted proteins would be expected in general to align more closely with bacterial than with archaeal or non-organellar eukaryote proteins. That prediction has been borne out. The hypothesis has been strengthened by that observation. How can that be? I did the same a few days ago with N-formyl methionine as translation initiator. Maybe I’m cherry-picking, but there are no searches I’m not mentioning that drew a blank. This is the sum total of my ‘research’: two things that it occurred to me to look for, and I found them both.

Also of interest to me, given the conviction explored in my ‘Evolution of Sex’ paper that meiosis is foundational to the modern eukaryote clade, is the finding that Dmc1 apparently evolved very early during what it pleases me to call ‘eukaryogenesis’. Whether it preceded or succeeded the mitochondrial endosymbiosis is not clear, which is one reason I don’t think of endosymbiosis as definitively the origin of the eukaryotic cell, whatever lols may accompany someone finding an author who does just that (Hi, Mung!).

Another point to ponder: homologous recombination relies upon a physical analogue of the algorithmic alignment performed during sequence comparison. It is only by anchoring matching sequences that ‘differences’ – in repair, the missing vs the intact sequence – can be located. Molecular differences between taxa are trumpeted by Creationists, but they are located in much the same way. The question remains: where does the alignment come from? In the case of sister chromosomes, it is non-controversially common descent – the sisters arise in the same cell cycle. In the case of diploid homologues, again not too controversial – the bases of the haploid chromosomes in gametes can reasonably be assumed to have a common origin in template-copies originating in an ancestral cell. But somehow, for the Creationist, this logic breaks down somewhere not clearly specified outside of the species. Alignment suddenly stops being common descent and becomes the completely indistinguishable ‘common design’. I don’t see why.

More than twenty different endosymbiotic theories were presented for the origin of the eukaryotes. They all agree in that endosymbiosis was important, perhaps even crucial in eukaryogenesis though there is no agreement in the nature of the host or the endosymbiont, and in the order of events, which are hidden behind the event horizon of the last eukaryotic common ancestor (LECA).

The claim is that such a parasitic invasion would be non-fatal and a symbiotic relationship would be born.

The infection is non-fatal in a majority of the infected individuals. I’m not sure why you think that DNA incorporation from intracellular parasites would constitute, or be expected to, form a symbiotic relationship.

the questions you proposed made no mention of any symbiotic relationship. They appear only to be a query regarding known instances of parasite transfer of DNA and subsequent integration into the human genome.

And by homologous you mean a similar sequence due to sharing a common ancestor? How do you suppose that the repair machinery detects whether the degree of identity is due to common ancestry?

As I pointed out, there is something of a terminological confusion here. Yeah, those evolutionists and their words … but really, it’s genetics and biochemistry too. There is not the equivalent of l’Academie Francaise to keep everyone on track. ‘Homologous’ chromosomes are the two parental copies. That’s not a statement about common ancestry, though it would be an unusual position to deny that sites within them were commonly descended. ‘Homologous sequence’, likewise, just means complementary sequence, not necessarily commonly descended. Why didn’t I use that term instead? Convention. Either will do.

So, thinks I, if chloroplasts and mitochondria were designed to have similarities to bacteria, their ReCA equivalents should be more like those of bacteria than archaea.

Would you have thought to have made the assumption that mitochondria were designed to be similar to bacteria, were you not conducting a rearguard action against an evolutionary prediction? This is the ‘cargo cult’ nature of Creationism on display, always playing catch-up. Evolutionist – “if X happened, I would expect Y”. Creationist: “Yeah! Yeah, that’s what I’d expect too!”. Like hell you would.

So then how do you explain eukaryotic chromatin-like fibers in archaea yet eukaryotic RecA equivalents in bacteria but not in archaea! Are you arguing chromatin is more ancient than homologous repair?

Not sure why you need to ask. If mitochondria originated from alpha-proteobacteria, then proteins targeted to those organelles ought to align with those taxa more often than with other taxa. Not necessarily universally, but there should be a bias. Same argument for chloroplasts and cyanobacteria.

Why are you looking at anything other than single-cell eukaryotes though? Any thoughts about differences in DNA repair strategies in cases without two parents? I’m basically asking you to humor me. I like to keep things simple and basic and not introduce anything more complex onto the scene than is really needed.

Can we stick to single-celled (unicellular) organisms and how they handle DNA repair?

So chloroplasts were in the common ancestor of all eukaryotes but then got lost in the lineage that led to animals? Why wasn’t that predicted?

It’s not even thought to be the case. A second endosymbiosis event in the lineage leading to plants brought in a cyanobacterium and its genes, is the hypothesis. It’s not predicted, it makes a prediction.

I think you’re confusing the chloroplast with a lineage-specific loss of a recA gene targeted to mitochondria. Possibly.

Allan Miller: If mitochondria originated from alpha-proteobacteria, then proteins targeted to those organelles ought to align with those taxa than with other taxa. Not necessarily universally, but there should be a bias. Same argument for chloroplasts and cyanobacteria.

ok, but that seems to me like it’s just a restatement. I know Alan Fox doesn’t appreciate why questions, but I like why questions.

I guess I need to understand why the proteins that deal with mitochondrial DNA should be so different. What’s so different about mitochondrial DNA and chloroplast DNA as compared to nuclear DNA?

Put another way, a protein that evolved to process nuclear DNA would not work on any other kind of DNA because …

It’s a fair question. One simple answer is ‘homology’. A pair of sister chromosomes is almost identical. Homologues, less so. So when HR is in operation, and is ‘searching’ (let’s not, shall we? 🙂 ) for homologous sequence, there is more of it in the sisters than in the homologues (confusingly, as I say). Another possibility is proximity. Just-replicated chromosomes (sisters) are physically close or even joined. Homologues occupy separate chromosome ‘territories’ from which they glare at each other suspiciously.

Why are you looking at anything other than single-cell eukaryotes though? Any thoughts about differences in DNA repair strategies in cases without two parents? I’m basically asking you to humor me. I like to keep things simple and basic and not introduce anything more complex onto the scene than is really needed.

The strategies in biparental and monoparental organisms are about the same. In both cases, HR strongly prefers ‘sister’ chromosomes (in prokaryotes, no choice). It makes sense to repair from an identical copy. In diploids, the secondary pathway is actually NHEJ – nonhomologous end joining. That could lose something vital, but one assumes that this is less damaging than using the homologue on the average.

Can we stick to single-celled (unicellular) organisms and how they handle DNA repair?

I don’t really see any reason to. Arabidopsis, my ‘type plant’ in the OP is multicellular. Anyway there’s not much different going on as regards either repair or organelles.

I guess I need to understand why the proteins that deal with mitochondrial DNA should be so different. What’s so different about mitochondrial DNA and chloroplast DNA as compared to nuclear DNA?

The million dollar question! If you were designing, you wouldn’t go for two (or more) different ways of doing things. One might talk of ‘redundancy’, I suppose.

There may be physical constraints. Nuclear DNA is spooled on histones, and is divided into readily accessible ‘euchromatin’ and more tightly packed ‘heterochromatin’ ***. Organellar DNA is organised into structures called ‘nucleosomes’, reminiscent of those of bacteria (hmmmm…!). So one might need different proteins to deal with those different architectures. But why, one might ask, the different architectures?

*** Thinking on, another possible reason why homologues are generally not used for repair, but can be accessed by a ‘repair-like’ process during crossover in meiosis.

Allan Miller: But, just to point out, the topic is not really repair at all, but the phylogenetic signals associated with proteins that happen to be involved in repair.

Right. One hypothesis is that the DNA from the organelles somehow was transferred into the nuclear DNA. I’m wondering why that hypothesis is to be favored over a different one, say, that gene duplication took place in the nuclear DNA and the new gene evolved to work on the DNA of the organelles, with of course natural selection operating to make it like the original protein. A case of convergence.

Because so many chloroplast genes have been moved to the nucleus, many proteins that would originally have been translated in the chloroplast are now synthesized in the cytoplasm of the plant cell. These proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes.

Curiously, around half of the protein products of transferred genes aren’t even targeted back to the chloroplast.

So… Allan … How do you think this acquisition and loss came about? […]

Two models strike me as higher on the list than others. One is represented by Wolbachia (look it up!). That’s a bacterium which lives inside its host’s cytoplasm. Many genes have been transferred to the nucleus, and it exhibits many of the habits of mitochondria, such as preferring female lineages. It doesn’t seem a stretch at all to suppose that endosymbiosis started in similar fashion. In some cases, the association is parasitic, in others it actually appears to confer a benefit.

Another possibility is the Ignicoccus/Nanoarchaeon (look it up!) system of ectosymbiosis. Again, there is extensive gene transfer, in both directions, and in this case the export of ATP from one cell to another. And again, not such a stretch to suppose that the transport systems between cells in this system could still work if the smaller became surrounded by the larger’s cytoplasm.

(Incidentally, this comment had a lot of scare quotes. I took them out. Anticipating gotchas is such a ball-ache).

Just catching up, I see extensive discussion on ‘why’ organelle DNA would migrate to the nucleus.

Pray withhold your customary contempt for the following evolutionary explanation(s).

A common theme when multiple genomes exist inside a cell is that of genetic conflict. Natural selection does not just act at one level – the whole cell – but there are subdivisions which can act in their own ‘interests’ too. Ultimately, if the cell dies, all bets are off in sub-contests too. But given host competency, there is a tussle for control of the metaphorical wheel among the various genomes. The optimal strategy for one genome is not that for all. I would argue that a plant cell, for example, contains 4 genomes – 2 haploid, plus mitochondria plus chloroplasts. The battles between the haploid genomes are between partners of approximately equal strength (see my ‘evolution of sex’ paper!).

For organelles, there are two dynamics to consider: battles for control of strategy against the nuclear genome, and battles against other organelles of the same type. Mitochondria can be seen as competitive bacteria whose environment is the cytoplasm of the host. Any edge they can gain over each other will see the fitter type (yes! I said it!) proliferate. But, if that proliferation is at the expense of the host cell, the host cell itself is selected against – host cells that are not suffering damaging competition between their mitochondria will outcompete host cells that are.

Now, a gene that allows a mitochondrion to gain an edge must come from a mutation of the mitochondrial genome. So, any reduction of the mitochondrial genome reduces the opportunity for such a mutation to arise.

Minimally, you’d need a 2 stage process.
Stage 1 is leakage from damaged mitochondria and uptake by the nucleus.
Stage 2 is deletion of the mitochondrial copy in just one mitochondrion.

Provided the nuclear copy complements the function of the deleted copy, such that the latter is genuinely redundant, the population of mitochondria is likely to be taken over by the deleted version. Why? Because its mitochondria can be reproduced more quickly. Their DNA is shorter. This is why bacteria don’t have much junk.

Why haven’t all genes moved? The core genome of a mitochondrion contains the tRNAs and bits of ribosome for translating its own proteins, those being some core components of the oxidative phosphorylation process – the proteins by means of which the mitochondrion genetrates ATP. Nick Lane proposes (/suggests/hypothesises/surmises/reckons) that this enables individual mitochondria to respond much more rapidly to aerobic demands than having an extra step of nuclear transcription and export, then cytoplasmic translation and targeting. I think he’s right.

I know (God, do I know!) that the foregoing will be dismissed as so much evolutionary ‘fairy-tale’ by the opposition. Nonetheless, I invite people to attack the basic logic of the scenario anyway, rather than just knee-jerk.

Allan Miller: This is the ‘cargo cult’ nature of Creationism on display, always playing catch-up. Evolutionist – “if X happened, I would expect Y”. Creationist: “Yeah! Yeah, that’s what I’d expect too!”. Like hell you would.

You are accusing creationists of this? That’s amusing. The entire field of Lucky Accidents is full of people claiming every new discovery is a prediction of Lucky Accidents.

Junk DNA, we predicted that. No junk DNA, we predicted that too! Slow single step evolution? Yep! Fast evolution leaps-We thought of that! Convergent evolution? Of course, makes sense! There is positively no end to the revisions that Lucky Accidenters make to their theory, that they don’t claim as a prediction.

You are accusing creationists of this? That’s amusing. The entire field of Lucky Accidents is full of people claiming every new discovery is a prediction of Lucky Accidents.

That’s not the case. For example, endosymbiosis is not a prediction of anything – certainly not of evolutionary theory nor the ‘gradualist’ school thereof. It was a bit of a surprise, indeed (same goes for junk). Endosymbiotic theory was devised to explain certain facts, empirically discovered. But, if true, it makes predictions about what additional evidence we might find if we look. This indeed is what the whole OP was about. If endosymbiotic theory were true, I expected to find clustering of mitochondrial and chloroplast RecA proteins with the respective putative groups from which the endosymbiont arose. I found that: +1 for endosymbiotic theory. Ditto N-formyl methionine.

On the other hand, Sal would never have thought, in a million years, to look for things that aligned with ‘design theory’ in that way. The bacterial patterns I found were not a prediction of ‘design theory’. But they were a prediction of the endosymbiotic theory.

Here is another, quite subtle, reason why we find more mitochondrial/chloroplast genes in nuclei than in the organelles. It relates back to my ‘evolution of sex’ interests.

With the advent of sex, we have two different paths for genes to take. Because of the crossover of meiosis, which affects only the nuclear genome, segments of genome are removed from their genetic background in each life and placed in others. Over successive generations, this exposes individual loci to selection much more strongly than would otherwise be the case when they are perpetually chained to others. In an asexual genome (such as that of the mitochondrion) advantageous alleles are held back by their genetic context. The entire genome is an evolutionary allele; in recombining nuclear genes, the alleles are individual loci.

So, if a gene in a mitochondrion finds its way into the nucleus, it has found a short cut into the population. If such an allele is advantageous, it can spread throughout the population by selection. The future population can fix that allele more-or-less independently of all others. If, on the other hand, the gene copy remains only in the mitochondrion, any advantage it confers is restricted by the genome-fellows to which it is chained. Those less advantageous alleles are themselves purged from the population more efficiently if they are in the nucleus. These are in fact two sides of the same coin – the very terms ‘advantageous’ and ‘detrimental’ refer to alleles of a locus, and are relative terms each dependent on the other. If you have an advantageous allele, its allele is detrimental, and vice versa.

An advantageous variant in a mitochondrion can only get into the entire population if the host cell within which it occurs is ancestral to the entire future population. Its fate is tied to that of the rest of the mitochondrial genome, which is itself restricted to just one lineage. By migrating to the nucleus***, it can get into the population much more quickly. One would therefore expect the population to become dominated by nuclear versions of mitochondrial genes (‘one’ being me, at least!). To the extent that the nuclear version is being tuned much more rapidly than its mitochondrial equivalent, deletions of the ‘frozen’ gene in the mitochondrion might themselves be beneficial, in addition to the saving of replication cost noted in my previous post.

***One should not get carried away with the idea that genes ‘want’ to take this route. It is simply the case that, if they do so, passively, they become swept into the ‘main line’ of vertical descent, which has a different dynamic from the mitochondrial fate.

If you don’t think its the case, then that is only because you don’t get around much. You could come up with a 100 examples of times when some new aspect of evolution is found, be it the rapid evolution of Italian wall lizards, be it in the discovery of the epigenome, be it in convergent evolution, or the size of the human genome compared to a mice, or in the species found in the Cambrian..it never ends. First, they report it as a surprise, but then it is quickly followed by the dirth of scientists saying, “Well, actually its to be expected, if there is selection pressure on a lizard, they will adapt within months, its nature!….blah blah”

Lucky Accidenters seem to not be very self aware of the load of ridiculous things they ask those who question the universe, to accept without thought.

Mung: Do you know what an event horizon is? That’s how they describe what took place before the LECA. We just don’t know and we can’t see.

Now you can continue to believe what you like, and tell stories all you like, but they are not evidence-based theories.

This doesn’t mean that goddidit. It just means that we’re ignorant. And we ought not pretend to know more than what we can currently know just because we need for something like our story to be true in order to be an intellectually fulfilled atheist.

Be a scientist, not a teller of tales. As long as you continue to tell tales I’ll be here to laugh at them, sure. I know they are just tales. Surely you know it too.

You don’t seem to understand that it is evidence that got us to where we are now. It is standard practice to make hypothesis that both explains the data you have collected, and makes further predictions about data you have yet to collect. This is how scientists got to the endosymbiosis hypothesis in the first place.

You’re welcome to try to come up with a better explanation that both explains all the same data as the endosymbiosis hypothesis, and also predicts what new data we have yet to collect should look like. You act as if what I have been telling you has no evidence for it, but many of these things are facts that were predicted on the basis of the endosymbiosis hypothesis and later confirmed either by observation (new genomes were sequenced for example), or by experiments and/or simulations.
It is too simplistic to say that we are at an event horizon beyond which we can’t observe. There are still many many species of microorganisms out there we can sequence, and the data we get from them will provide evidence for or against various competing hypotheses.

The recently sequenced Lokiarchaeota is a very good example of this, having versions of components previously thought to be unique to Eukaryotes, but predicted to have arisen in the ancestors of the archaeal host by some endosymbiotis hypotheses.

So you mean that this would be evidence against Darwinian evolution then?

No, I mean provide an example of that happening of which you say there are 100’s of cases – an evolutionist saying that endosymbiosis is just what evolutionary theory would predict. Or the lizards if you prefer. So far, you have just paraphrased a claim I’m doubtful has ever been made. It would be easy to show me wrong.

There are things that evolutionary theory predicts, but neither endosymbiosis nor ‘surprisingly fast’ evolution is among them.

The speed of any given instance of evolution is not predicted by evolutionary theory, IMO. I thought you were claiming someone said it was? In which case, a reference should be available in a jiffy.

Right, so I just showed you a quote from Darwin, where he claimed it would be slow steps, and now, after we now know that it doesn’t always happen in slow steps, you have revised the theories predictions, by claiming it makes no predictions about speed, so both fast or slow are acceptable expected outcomes of Darwinian evolution.